Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.

PubWeight™: 0.98‹?› | Rank: Top 15%

🔗 View Article (PMC 3185296)

Published in Cancer Genet on August 01, 2011

Authors

Oliver A Hampton1, Maxim Koriabine, Christopher A Miller, Cristian Coarfa, Jian Li, Petra Den Hollander, Caroline Schoenherr, Lucia Carbone, Mikhail Nefedov, Boudewijn F H Ten Hallers, Adrian V Lee, Pieter J De Jong, Aleksandar Milosavljevic

Author Affiliations

1: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. ohampton@bionanomatrix.com

Articles cited by this

Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63

Circos: an information aesthetic for comparative genomics. Genome Res (2009) 40.02

Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46

Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 30.28

Fine-scale structural variation of the human genome. Nat Genet (2005) 24.31

A comprehensive catalogue of somatic mutations from a human cancer genome. Nature (2009) 24.27

High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods (2009) 18.41

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (2009) 15.08

The genomic complexity of primary human prostate cancer. Nature (2011) 14.06

Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature (2009) 13.45

Segmental duplications: organization and impact within the current human genome project assembly. Genome Res (2001) 11.77

Transcriptome sequencing to detect gene fusions in cancer. Nature (2009) 11.63

Limitations of next-generation genome sequence assembly. Nat Methods (2010) 9.04

End-sequence profiling: sequence-based analysis of aberrant genomes. Proc Natl Acad Sci U S A (2003) 7.70

The BRCT domain is a phospho-protein binding domain. Science (2003) 7.42

Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res (2007) 6.91

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87

Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response. Science (2007) 5.88

Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30

BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell (2001) 5.05

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res (2007) 4.99

Molecular mechanisms for genomic disorders. Annu Rev Genomics Hum Genet (2002) 4.51

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47

Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res (2006) 4.25

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res (2008) 4.06

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A (2009) 2.57

Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs. Hum Mutat (2003) 2.55

High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A (2010) 2.47

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One (2011) 2.34

CCDC98 targets BRCA1 to DNA damage sites. Nat Struct Mol Biol (2007) 2.24

Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res (2006) 2.09

Genetic alterations and oncogenic pathways associated with breast cancer subtypes. Mol Cancer Res (2009) 2.05

Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer. Genes Chromosomes Cancer (2002) 2.04

Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. Nucleic Acids Res (2010) 1.95

Comprehensive genome sequence analysis of a breast cancer amplicon. Genome Res (2001) 1.74

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res (2011) 1.67

Role of RAD51C and XRCC3 in genetic recombination and DNA repair. J Biol Chem (2006) 1.56

Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res (2011) 1.30

ZNF217 suppresses cell death associated with chemotherapy and telomere dysfunction. Hum Mol Genet (2005) 1.25

Clinical significance of miR-21 expression in breast cancer: SYBR-Green I-based real-time RT-PCR study of invasive ductal carcinoma. Oncol Rep (2009) 1.16

Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer. BMC Genomics (2008) 1.14

Domain mapping of the Rad51 paralog protein complexes. Nucleic Acids Res (2004) 1.14

Scanning the human genome at kilobase resolution. Genome Res (2008) 1.13

Novel lipogenic enzyme ELOVL7 is involved in prostate cancer growth through saturated long-chain fatty acid metabolism. Cancer Res (2009) 1.12

Prognostic value of CCND1 gene status in sporadic breast tumours, as determined by real-time quantitative PCR assays. Br J Cancer (2002) 1.06

Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer. Breast Cancer Res (2005) 1.03

Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics (2007) 0.96

Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I--usefulness in SAGE. Biochem Biophys Res Commun (2005) 0.93

Germline RAP80 mutations and susceptibility to breast cancer. Breast Cancer Res Treat (2008) 0.92

Analysis of the genes coding for the BRCA1-interacting proteins, RAP80 and Abraxas (CCDC98), in high-risk, non-BRCA1/2, multiethnic breast cancer cases. Breast Cancer Res Treat (2008) 0.90

Optimizing PCR assays for DNA-based cancer diagnostics. J Comput Biol (2010) 0.80

Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics (2004) 0.79

Articles by these authors

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78

Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res (2012) 15.90

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature (2012) 14.33

The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99

The origin and evolution of mutations in acute myeloid leukemia. Cell (2012) 9.66

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature (2012) 8.03

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00

Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet (2009) 6.42

The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41

Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39

A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res (2009) 4.78

The Norway spruce genome sequence and conifer genome evolution. Nature (2013) 4.74

Estrogen receptor-positive, progesterone receptor-negative breast cancer: association with growth factor receptor expression and tamoxifen resistance. J Natl Cancer Inst (2005) 4.25

The genomic sequence of the accidental pathogen Legionella pneumophila. Science (2004) 4.08

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res (2008) 4.06

Neural correlates of behavioral preference for culturally familiar drinks. Neuron (2004) 3.80

Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis. J Clin Oncol (2008) 3.74

Myocardin is a critical serum response factor cofactor in the transcriptional program regulating smooth muscle cell differentiation. Mol Cell Biol (2003) 3.69

Biology of progesterone receptor loss in breast cancer and its implications for endocrine therapy. J Clin Oncol (2005) 3.62

Proteomic and transcriptomic profiling reveals a link between the PI3K pathway and lower estrogen-receptor (ER) levels and activity in ER+ breast cancer. Breast Cancer Res (2010) 3.53

Population pharmacokinetics of intravenous polymyxin B in critically ill patients: implications for selection of dosage regimens. Clin Infect Dis (2013) 3.49

An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics (2012) 3.41

Analyses and comparison of accuracy of different genotype imputation methods. PLoS One (2008) 3.41

Shared Genetic Predisposition in Peripartum and Dilated Cardiomyopathies. N Engl J Med (2016) 3.40

Expression of autotaxin and lysophosphatidic acid receptors increases mammary tumorigenesis, invasion, and metastases. Cancer Cell (2009) 3.36

Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat Methods (2009) 3.35

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol (2012) 3.31

Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science (2013) 3.17

Polymyxin B for the treatment of multidrug-resistant pathogens: a critical review. J Antimicrob Chemother (2007) 3.15

NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol (2008) 3.11

Carbapenem resistance in Klebsiella pneumoniae due to the New Delhi Metallo-β-lactamase. Clin Infect Dis (2011) 3.06

Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production. Antimicrob Agents Chemother (2010) 3.03

Colistin methanesulfonate is an inactive prodrug of colistin against Pseudomonas aeruginosa. Antimicrob Agents Chemother (2006) 2.95

Stimulation-dependent recycling of integrin beta1 regulated by ARF6 and Rab11. Traffic (2004) 2.91

Colistin hetero-resistance in multidrug-resistant Acinetobacter baumannii clinical isolates from the Western Pacific region in the SENTRY antimicrobial surveillance programme. J Infect (2008) 2.88

Pharmacokinetics of intravenous polymyxin B in critically ill patients. Clin Infect Dis (2008) 2.79

The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome (2012) 2.65

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology (2011) 2.60

Oncogenic transformation by the signaling adaptor proteins insulin receptor substrate (IRS)-1 and IRS-2. Cell Cycle (2007) 2.48

Central and autonomic nervous system interaction is altered by short-term meditation. Proc Natl Acad Sci U S A (2009) 2.45

Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell (2012) 2.43

Antiretroviral therapy to prevent HIV transmission in serodiscordant couples in China (2003-11): a national observational cohort study. Lancet (2012) 2.41

Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res (2003) 2.41

Temporal dissection of tumorigenesis in primary cancers. Cancer Discov (2011) 2.40

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One (2011) 2.34

DGIdb: mining the druggable genome. Nat Methods (2013) 2.26

MicroRNA-21 promotes fibrosis of the kidney by silencing metabolic pathways. Sci Transl Med (2012) 2.20

Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods (2013) 2.19

Short-term BMP-4 treatment initiates mesoderm induction in human embryonic stem cells. Blood (2007) 2.18

The role of the striatum in aversive learning and aversive prediction errors. Philos Trans R Soc Lond B Biol Sci (2008) 2.17

The price of racial bias: intergroup negotiations in the ultimatum game. Psychol Sci (2013) 2.15

Trainees' adenoma detection rate is higher if ≥ 10 minutes is spent on withdrawal during colonoscopy. Surg Endosc (2011) 2.15

Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells. Cell Stem Cell (2012) 2.11

Proinflammatory role for let-7 microRNAS in experimental asthma. J Biol Chem (2010) 2.08

Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet (2009) 2.07

AIB1/SRC-3 deficiency affects insulin-like growth factor I signaling pathway and suppresses v-Ha-ras-induced breast cancer initiation and progression in mice. Cancer Res (2004) 2.07

Intelligent urban public transportation for accessibility dedicated to people with disabilities. Sensors (Basel) (2012) 2.06

Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics (2011) 2.05

Structure--activity relationships of polymyxin antibiotics. J Med Chem (2010) 2.03

Hypercholesterolemia impairs the myocardial angiogenic response in a swine model of chronic ischemia: role of endostatin and oxidative stress. Ann Thorac Surg (2006) 2.02

What's in a smile? Maternal brain responses to infant facial cues. Pediatrics (2008) 2.02

Smooth muscle cells and myofibroblasts use distinct transcriptional mechanisms for smooth muscle alpha-actin expression. Circ Res (2007) 2.00

Regulation of apoptosis and differentiation by p53 in human embryonic stem cells. J Biol Chem (2006) 1.99

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One (2012) 1.98

Megakaryoblastic leukemia factor-1 transduces cytoskeletal signals and induces smooth muscle cell differentiation from undifferentiated embryonic stem cells. J Biol Chem (2004) 1.98

Colistin in the 21st century. Curr Opin Infect Dis (2009) 1.93

Improved breast cancer prognosis through the combination of clinical and genetic markers. Bioinformatics (2006) 1.93

Development and validation of a reversed-phase high-performance liquid chromatography assay for polymyxin B in human plasma. J Antimicrob Chemother (2008) 1.91

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol (2014) 1.90

Constitutively active type I insulin-like growth factor receptor causes transformation and xenograft growth of immortalized mammary epithelial cells and is accompanied by an epithelial-to-mesenchymal transition mediated by NF-kappaB and snail. Mol Cell Biol (2007) 1.89

The type I insulin-like growth factor receptor pathway: a key player in cancer therapeutic resistance. Front Biosci (2008) 1.88

Management of meningitis due to antibiotic-resistant Acinetobacter species. Lancet Infect Dis (2009) 1.87

A physical map of the chicken genome. Nature (2004) 1.86

Elucidation of the pharmacokinetic/pharmacodynamic determinant of colistin activity against Pseudomonas aeruginosa in murine thigh and lung infection models. Antimicrob Agents Chemother (2009) 1.83

GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PLoS Genet (2009) 1.83

A novel recessive Nefl mutation causes a severe, early-onset axonal neuropathy. Ann Neurol (2009) 1.83

Prospective study of tailoring whole-body dual-modality [18F]fluorodeoxyglucose positron emission tomography/computed tomography with plasma Epstein-Barr virus DNA for detecting distant metastasis in endemic nasopharyngeal carcinoma at initial staging. J Clin Oncol (2013) 1.81

Activity of colistin against heteroresistant Acinetobacter baumannii and emergence of resistance in an in vitro pharmacokinetic/pharmacodynamic model. Antimicrob Agents Chemother (2007) 1.81

A role for the melatonin-related receptor GPR50 in leptin signaling, adaptive thermogenesis, and torpor. Curr Biol (2011) 1.80

BioStar: an online question & answer resource for the bioinformatics community. PLoS Comput Biol (2011) 1.80